How do I keep two softbodies in the same position?
Two options:

Assign all verts in BigCube to a vertex group.  Give SmallCube a copy location constraint, targeting BigCube and referencing this vertex group.  Give SmallCube a healthy Goal value (or group).

Join BigCube and SmallCube into a single object.  Create edges (only) between BigCube and SmallCube to create forces between the two.  These will act as any other soft body edges, seeking to maintain their length (and possibly, with positive soft body bending values, lengths to neighbor verts), causing SmallCube to prefer to float inside of BigCube rather than fall completely to the ground.